export: export

In les: Identifying Differential Effects in Tiling Microarray Data

Description

Exports the results into files for interaction with other software. Estimated regions can be exported in 'bed' and 'gff' format, Lambda in 'wig' format.

Usage

export(object, file, format="bed", chr, range, description = "Lambda",
strand=".", group="les", precision=4, ...)

## S4 method for signature 'Les'
export(object, file, format="bed", chr, range,
description = "Lambda", strand=".", group="les", precision=4, ...)

Arguments

object	Object of class 'Les' containing experimental data, as returned by 'estimate' or 'regions'.
file	Character string specifying the file path and name for export.
format	Character string with the export format (default: 'bed'). Possible values are 'bed' and 'gff' for export of the estimated regions and 'wig' for export of Lambda for the probes. If set to 'bed' or 'gff' the method 'regions' has to be run beforehand. Partial matches are also possible. For details on the formats please see the 'Details' section.
chr	Character string specifying the chromosome from which results should be exported. This value must be set if exporting to 'wig' format, for other formats is optional. 'chr' must have exactly one match in the 'chr' argument specified in 'Les'.
range	Numeric vector specifying the range of probe positions which should be exported. If missing all probes of the chromosome will be exported. This value has only an effect if 'format' is set to 'wig'.
description	Character string with description for the exported track (default: 'Lambda'). This will be used as description by several programs and genome browsers.
strand	Character string with strand specification for 'gff' export (default: '.'). Possible values are '+', '-' or '.'.
group	Character string with group specifications of the resulting regions in 'gff' format (default: 'les').
precision	Integer specifying the number of digits Lambda should be rounded to for export to 'wig' format (default: 4).
...	Further arguments passed to subsequent functions.

Details

This function is useful to export the estimated Lambda to external programs and genome browsers.

The 'bed', 'gff' and 'wig' format provide widely used standard formats and are compatible with most genome browsers and related software. For details about the file formats see http://genome.ucsc.edu/FAQ/FAQformat.html.

Author(s)

Julian Gehring

Maintainer: Julian Gehring <[e-mail]>

See Also

Package: les-package

Class: Les

Methods and functions: Les estimate threshold regions ci chi2 export plot

Examples

## Not run: 
data(spikeInStat)

x <- Les(pos, pval)
x <- estimate(x, 200)
x <- threshold(x)
x <- regions(x)

export(x, file="test.bed")
export(x, file="test.gff", format="gff")
export(x, file="test.wig", format="wig", chr=0)

## End(Not run)

les documentation built on Nov. 8, 2020, 5:17 p.m.